On 1/3/13 6:11 AM, Shima Arasteh wrote:
Have a look at CT2 in aminoacids.c.tdb please:
[ CT2 ]
[ replace ]
O CC 12.011 0.55
O O 15.9994 -0.55
It is +0.55 as what you said. But I see all carbonyl C in aminoacids.rtp file
have +0.51 charge.
I think the amidated C-terminal in my top file should be charged +0.55 as what
I see in c.tdb. Shouldn't be? Why it couldn't understand to take +0.55 charge
for this last residue?
There is an error in the .tdb file. The first [replace] line attempts to
replace an O atom and assign it a CC type with charge of +0.55, which is then
overridden by the next line, which assigns the O atom an O type with -0.55
charge. The carbonyl C is (erroneously) not adjusted. The correct line is
present in the charmm27.ff folder:
[ CT2 ]
[ replace ]
C CC 12.011 0.55
O O 15.9994 -0.55
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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